How can I have separated Layers in Texture painting in cycles?
The related comment that cegaton provided shows an answer (via a screenshot of the cycles node editor) in the link that identifies how to add more than one image texture to affect your material.

I think more specifically to you is how to manage this in texture paint mode.
The easy answer is add all of the images you wish to use for all of your different reasons first. 


If these images do not exist you need to create them as new images in the UV/Image editor and save them to a file first.
You can do this in the node editor if these images already exist by just adding the Texture >> Image Texture node, and selecting that image in the dropdown selection of the node.


Once you have all of your images in your blend, you just need to make sure that they are present in your material.

They need not be connected to anything yet, it just needs to exist.
Once they exist go into texture paint mode within the 3D viewport, and manage the active image by selecting it via the slots tab on the T menu at left.